Microbial resources from the human gut may find use in various applications, such as empirical research on the microbiome, the development of probiotic products, and bacteriotherapy. Due to the development of “culturomics”, the number of pure bacterial cultures obtained from the human gut has significantly increased since 2012. However, there is still a considerable number of human gut microbes to be isolated and cultured. Thus, to improve the efficiency of obtaining microbial resources from the human gut, some constraints of the current methods, such as labor burden, culture condition, and microbial targetability, still need to be optimized. Here, we overview the general knowledge and recent development of culturomics for human gut microorganisms. Furthermore, we discuss the optimization of several parts of culturomics including sample collection, sample processing, isolation, and cultivation, which may improve the current strategies.
Background The oral cavity is the second most microbially rich region of the human body, and many studies show a strong association between microorganisms and oral health. Some pathogenic bacteria produce biofilms and harmful metabolites in the mouth that may cause oral problems including oral malodour, periodontitis, and dental caries. Interestingly, intervening with oral microbiota through probiotics may alleviate oral problems. Thus, we hope to obtain probiotics that can significantly improve oral health through multi-target screening. Results We found that Bifidobacterium animalis ZK-77 (B. animalis ZK-77), Lactobacillus salivarius ZK-88 (L. salivarius ZK-88) and Streptococcus salivarius ZK-102 (S. salivarius ZK-102) can enhance the antibacterial ability and inhibit biofilm production to prevent tooth caries. Besides, they were of significant capacity for improving the indicators of oral malodour including the production of H2S, NH3, and indole. The selected probiotics intervening suggested that they could alleviate the inflammatory situation in the oral cavity of rats with periodontitis, especially L. salivarius ZK-88. The analysis of the alveolar fluid microbiome after probiotic intervention showed that B. animalis ZK-77 was likely to help restore the oral microbiota and maintain the oral microecology. Then, we rationally matched the candidate probiotics strains with prebiotics to obtain a combination with a better effect, and found that the probiotics combination has a significant effect on improving halitosis and teeth color in cats. Through whole genome sequence analysis of the candidate strains, we found that neither strain had virulence genes, which revealed the safety of them. Conclusion Taken together, we screened B. animalis ZK-77 and L. salivarius ZK-88 that can improve oral health and verified their functions through in vivo and in vitro experiments. This work provides some reference for clinical research and also provides new support for the use of probiotics in oral health.
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